new force field option

diff --git a/django_simple/todo/forms.py b/django_simple/todo/forms.py
index d8ea95d..987887b 100644 (file)
--- a/django_simple/todo/forms.py
+++ b/django_simple/todo/forms.py
@@ -3,6 +3,7 @@ from .models import Task
 from .models import MIN_CHOICE
 from .models import MD_START
 from .models import MD_LANG
+from .models import FF_CHOICE
 import json
 
 class MultiWidgetBasic(forms.MultiWidget):
@@ -49,6 +50,8 @@ class TaskForm_min(forms.Form):
 class TaskForm_min_a(forms.Form):
      name = forms.CharField(max_length=20)
 
+     unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
+                           label='Force Field',initial='E0LL2Y')
      min_choice = forms.ChoiceField(choices=MIN_CHOICE,label='minimization algorithm')
      min_overlap = forms.BooleanField(required=False,label='remove overlap')
      min_searchsc = forms.BooleanField(required=False,label='MC for sidechain overlap')
@@ -109,6 +112,8 @@ class TaskForm_md(forms.Form):
 class TaskForm_md_a(forms.Form):
      name = forms.CharField(max_length=20)
 
+     unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
+                           label='Force Field',initial='E0LL2Y')
      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
                       label='starting structure',initial='extconf')
      md_seq = forms.CharField(label='Sequence',
@@ -203,6 +208,8 @@ class TaskForm_remd(forms.Form):
 class TaskForm_remd_a(forms.Form):
      name = forms.CharField(max_length=20)
 
+     unres_ff = forms.ChoiceField(choices=FF_CHOICE,widget=forms.RadioSelect,
+                           label='Force Field',initial='E0LL2Y')
      md_start = forms.ChoiceField(choices=MD_START,widget=forms.RadioSelect,
                       label='starting structure',initial='extconf')
      md_seq = forms.CharField(label='Sequence',

diff --git a/django_simple/todo/jobfiles.py b/django_simple/todo/jobfiles.py
index 2b16ba3..ce0cf44 100644 (file)
--- a/django_simple/todo/jobfiles.py
+++ b/django_simple/todo/jobfiles.py
@@ -41,12 +41,21 @@ def write_on_task_save(sender, instance, **kwargs):
 #wrapper = textwrap.TextWrapper(width=70)
 #word_list = wrapper.wrap(text=md.substitute(nstep=str(nstep)))
 
-     w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954              &
+     if  instance.unres_ff =='E0LL2Y':
+      w="""WSC=1.00000 WSCP=1.23315 WELEC=0.84476 WBOND=1.00000 WANG=0.62954              &
 WSCLOC=0.10554 WTOR=1.34316 WTORD=1.26571 WCORRH=0.19212 WCORR5=0.00000        &
 WCORR6=0.00000 WEL_LOC=0.37357 WTURN3=1.40323 WTURN4=0.64673 WTURN6=0.00000    &
 WVDWPP=0.23173 WHPB=1.00000 WSCCOR=0.25                                        &
 CUTOFF=7.00000 WCORR4=0.00000
 """
+     else:
+      w="""WSC=0.82686 WSCP=0.96947 WELEC=0.79373 WBOND=1.00000 WANG=0.46542              &
+WSCLOC=0.07969 WTOR=0.81684 WTORD=0.67806 WCORRH=0.00000 WCORR5=0.00000        &
+WCORR6=0.00000 WEL_LOC=0.71100 WTURN3=2.30298 WTURN4=0.86517 WTURN6=0.00000    &
+WSCCOR=0.14577 WVDWPP=0.17781 WHPB=1.00000 WSCP14=0.00000                      &
+CUTOFF=7.00000 WCORR4=0.00000
+"""
+     
 
      with open(instance.jobdirname+'/file.inp','w') as f:
        f.write(instance.name + ' UNRES server job'+ '\n')
@@ -206,12 +215,18 @@ CUTOFF=7.00000 WCORR4=0.00000
         
      if instance.type == 'min':
       os.chdir(instance.jobdirname)
-      shutil.copy('../files/pbs.csh','.')
+      if  instance.unres_ff =='E0LL2Y':
+        shutil.copy('../files/pbs.csh','.')
+      else:
+        shutil.copy('../files/pbs_new.csh','pbs.csh')
       ret_code = subprocess.Popen(' /opt/torque/bin/qsub pbs.csh', shell=True, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
       os.chdir('..')
      elif instance.type == 'md':
       os.chdir(instance.jobdirname)
-      f1 = open('../files/pbs_md.csh', 'r')
+      if  instance.unres_ff =='E0LL2Y':
+        f1 = open('../files/pbs_md.csh', 'r')
+      else:
+        f1 = open('../files/pbs_md_new.csh', 'r') 
       f2 = open('pbs.csh', 'w')
       for line in f1:
            f2.write(line.replace('$dimen3',str(dimen3) ))
@@ -238,7 +253,10 @@ CUTOFF=7.00000 WCORR4=0.00000
         pbs = '#PBS -l nodes='+str(nodes)+':ppn=4+1:ppn='+str(reszta)
 
       os.chdir(instance.jobdirname)
-      f1 = open('../files/pbs8.csh', 'r')
+      if  instance.unres_ff =='E0LL2Y':
+        f1 = open('../files/pbs8.csh', 'r')
+      else:
+        f1 = open('../files/pbs8_new.csh', 'r')
       f2 = open('pbs8.csh', 'w')
       for line in f1:
           if '#PBS -l nodes=4:ppn=4' in line:

diff --git a/django_simple/todo/models.py b/django_simple/todo/models.py
index 295a84a..5177996 100644 (file)
--- a/django_simple/todo/models.py
+++ b/django_simple/todo/models.py
@@ -9,6 +9,7 @@ import json
 MIN_CHOICE = (('minimize cart','minimize'),('minimize regular','regularize'),('minimize softreg','soft regularize'),('minimize','minimize internal coordinates'))
 MD_START= (('extconf','extended chain'),('pdbstart','start from pdb'),('rand_conf','random chain'))
 MD_LANG = (('langevin','Langevin'),('berendsen','Berendsen'))
+FF_CHOICE = (('E0LL2Y','JCC 30 2127 (2009) + JCTC 11 817831 (2015)'),('opt-wtfsa-2','JCIM 10.1021/acs.jcim.7b00254 (2017)'))
 
 logger = logging.getLogger(__name__)
 
@@ -28,6 +29,7 @@ class Task(models.Model):
     def getssbond(self):
        return json.loads(self.ssbond)
 
+    unres_ff = models.CharField(max_length=20,choices=FF_CHOICE,default='E0LL2Y')
 # minimization
     min_choice = models.CharField(max_length=20,choices=MIN_CHOICE,default='minimize cart')
     min_overlap = models.BooleanField(default=False)

diff --git a/django_simple/todo/templates/details.html b/django_simple/todo/templates/details.html
index f9651c0..b69ff1b 100644 (file)
--- a/django_simple/todo/templates/details.html
+++ b/django_simple/todo/templates/details.html
@@ -20,6 +20,11 @@ Created {{ task.created_date  }}
                            <div class="col-xs-10"> type </div>
                            <div class="col-xs-10">{{ task.type }}</div>
                        </li>           
+         
+                       <li class="list-group-item task-item">
+                           <div class="col-xs-10"> force field </div>
+                           <div class="col-xs-10">{{ task.unres_ff }}</div>
+                       </li>           
 
                        <li class="list-group-item task-item">
                            <div class="col-xs-10"> sequence </div>
@@ -206,6 +211,11 @@ Created {{ task.created_date  }}
                            <div class="col-xs-10"> multiplex </div>
                            <div class="col-xs-10">{{ task.remd_multi_m}}</div>
                        </li>           
+                       <li class="list-group-item task-item">
+                           <div class="col-xs-10"> temperature for clustering</div>
+                           <div class="col-xs-10">{{ task.remd_cluter_temp}}</div>
+                       </li>           
+
 
         {% endif %}
 

diff --git a/django_simple/todo/views.py b/django_simple/todo/views.py
index 2d888e2..6f3a75e 100644 (file)
--- a/django_simple/todo/views.py
+++ b/django_simple/todo/views.py
@@ -125,6 +125,7 @@ def add_min_a(request,task_id):
              task.min_pdbout=form.cleaned_data["min_pdbout"]
              task.myfile1=form.cleaned_data["file1"]
              task.min_unres_pdb=form.cleaned_data["min_unres_pdb"]
+             task.unres_ff=form.cleaned_data["unres_ff"]
 
              seq,task.ssbond=from_pdb(task.myfile1)
              task.md_seq=""
@@ -222,7 +223,7 @@ def add_md_a(request,task_id):
              task.md_tau=form.cleaned_data["md_tau"]
              task.md_scal_fric=form.cleaned_data["md_scal_fric"]
              task.md_mdpdb=form.cleaned_data["md_mdpdb"]
-
+             task.unres_ff=form.cleaned_data["unres_ff"]
              
              task.ready=True
              basename = str(task.owner)
@@ -316,6 +317,7 @@ def add_remd_a(request,task_id):
 #             task.remd_rest1file=form.cleaned_data["remd_rest1file"]
 
              task.remd_cluter_temp=form.cleaned_data["remd_cluter_temp"]
+             task.unres_ff=form.cleaned_data["unres_ff"]
              
              basename = str(task.owner)
              suffix = datetime.datetime.now().strftime("%y%m%d_%H%M%S")

diff --git a/files/pbs8_new.csh b/files/pbs8_new.csh
new file mode 100755 (executable)
index 0000000..0382652
--- /dev/null
+++ b/files/pbs8_new.csh
@@ -0,0 +1,88 @@
+#PBS -N test_server
+#PBS -q nowy
+#PBS -l nodes=4:ppn=4
+
+#-----------------------------------------------------------------------------
+setenv UNRES_BIN /users2/czarek/UNRES/git3_tmp/build/bin/unresMD-mult_ifort_MPI_E0LL2Y.exe
+#-----------------------------------------------------------------------------
+setenv DD /users2/czarek/UNRES/git3_tmp/unres/PARAM
+setenv BONDPAR $DD/bond_AM1_ext_dum.parm
+setenv THETPAR $DD/theta_abinitio-ext-old.parm
+setenv THETPARPDB $DD/thetaml_ext.5parm
+setenv ROTPARPDB $DD/scgauss_ext.parm
+setenv ROTPAR $DD/rotamers_AM1_aura_ext.10022007.parm
+setenv TORPAR $DD/tor_opt_iter1_7p_old-ext.parm
+setenv TORDPAR $DD/pot_tord_G631_DIL_ext.parm
+setenv ELEPAR $DD/electr_631Gdp_ext.parm
+setenv SIDEPAR $DD/sc_GB_opt_iter1_7p_old-ext_lip.parm
+setenv FOURIER $DD/fourier_opt_iter1_7p_old-ext.parm
+setenv SCCORPAR $DD/sccor_am1_pawel_ext.dat
+setenv SCPPAR $DD/scp_ext.parm
+setenv PATTERN $DD/patterns.cart
+setenv LIPTRANPAR $DD/Lip_tran_initial_ext.parm
+#-----------------------------------------------------------------------------
+cd $PBS_O_WORKDIR
+
+setenv MPIRUN "/users2/local/mpich2-1.4.1p1_intel/bin/mpirun "
+set NPROCS=`cat $PBS_NODEFILE | wc -l`
+
+setenv FGPROCS 2
+setenv POT GB
+setenv PREFIX file
+setenv OUT1FILE YES
+
+#UNRES MREMD
+$MPIRUN -machinefile $PBS_NODEFILE -np $NPROCS $UNRES_BIN
+
+#WHAM
+setenv WHAM_BIN /users2/czarek/UNRES/git3_tmp/build/bin/wham-mult_ifort_MPI_E0LL2Y.exe
+setenv CONTFUNC GB
+setenv SIDEP $DD/contact_ext.3.parm
+setenv SCRATCHDIR .
+setenv PREFIX file_wham
+
+$MPIRUN -machinefile $PBS_NODEFILE -np 2 $WHAM_BIN
+
+#test images
+setenv line `awk '{}END{print int(NR*0.2)}' file_GB000.stat`
+
+if ( `grep -c pdbref file.inp` ) then
+ tail -q -n +$line file_GB*.stat |  awk '{if ( NF == 14 ) print}' >remd_all.stat
+ cat file_GB*.stat |  awk '{if ( NF == 14 ) print}' > remd_all0.stat
+else
+ tail -q -n +$line file_GB*.stat |  awk '{if ( NF == 10 ) print}' >remd_all.stat
+ cat file_GB*.stat |awk '{if ( NF == 10 ) print}' > remd_all0.stat
+endif
+../files/matplotlib_hist.py $temperatures
+rm remd_all.stat remd_all0.stat
+
+#CLUSTER WHAM
+setenv INPUT file_cluster
+setenv INTIN file_wham
+setenv OUTPUT file_cluster
+setenv PDB CART
+setenv COORD CX
+setenv PRINTCOOR PRINT_PDB
+setenv CLUSTER_WHAM_BIN /users2/czarek/UNRES/git3_tmp/build/bin/cluster_wham-mult_ifort_MPI_E0LL2Y.exe
+
+$MPIRUN -machinefile $PBS_NODEFILE -np 2 $CLUSTER_WHAM_BIN
+
+ln -s file_wham_T*K_ave.pdb ave
+../files/cluster2allatom.sh ave
+rm ave
+
+#amber min refinement
+foreach i (`seq 1 5`)
+../files/refine.sh MODEL$i.pdb
+end
+
+/users2/local/pymol_1.6/pymol -c ../files/model.pml
+
+/users2/local/bin/tmscore MODEL1.pdb plik.pdb > tmscore1.out
+/users2/local/bin/tmscore MODEL2.pdb plik.pdb > tmscore2.out
+/users2/local/bin/tmscore MODEL3.pdb plik.pdb > tmscore3.out
+/users2/local/bin/tmscore MODEL4.pdb plik.pdb > tmscore4.out
+/users2/local/bin/tmscore MODEL5.pdb plik.pdb > tmscore5.out
+
+#END
+touch finished

diff --git a/files/pbs_md.csh b/files/pbs_md.csh
index d5344d9..8acaec5 100755 (executable)
--- a/files/pbs_md.csh
+++ b/files/pbs_md.csh
@@ -39,7 +39,7 @@ else
  awk '{if ( NF == 10 ) print}' file_GB000.stat > md.stat
 endif
 
-../../files/matplotlib_fit_hist.py $dimen3
+../files/matplotlib_fit_hist.py $dimen3
 rm md.stat
 
 if ( -f "file_MD000.pdb" ) then

diff --git a/files/pbs_md_new.csh b/files/pbs_md_new.csh
new file mode 100755 (executable)
index 0000000..6a678a8
--- /dev/null
+++ b/files/pbs_md_new.csh
@@ -0,0 +1,58 @@
+#PBS -N test_server
+#PBS -q express
+#PBS -l nodes=1:ppn=4
+
+#-----------------------------------------------------------------------------
+setenv UNRES_BIN /users2/czarek/UNRES/git3_tmp/build/bin/unresMD-mult_ifort_MPI_E0LL2Y.exe
+#-----------------------------------------------------------------------------
+setenv DD /users2/czarek/UNRES/git3_tmp/unres/PARAM
+setenv BONDPAR $DD/bond_AM1_ext_dum.parm
+setenv THETPAR $DD/theta_abinitio-ext-old.parm
+setenv THETPARPDB $DD/thetaml_ext.5parm
+setenv ROTPARPDB $DD/scgauss_ext.parm
+setenv ROTPAR $DD/rotamers_AM1_aura_ext.10022007.parm
+setenv TORPAR $DD/tor_opt_iter1_7p_old-ext.parm
+setenv TORDPAR $DD/pot_tord_G631_DIL_ext.parm
+setenv ELEPAR $DD/electr_631Gdp_ext.parm
+setenv SIDEPAR $DD/sc_GB_opt_iter1_7p_old-ext_lip.parm
+setenv FOURIER $DD/fourier_opt_iter1_7p_old-ext.parm
+setenv SCCORPAR $DD/sccor_am1_pawel_ext.dat
+setenv SCPPAR $DD/scp_ext.parm
+setenv PATTERN $DD/patterns.cart
+setenv LIPTRANPAR $DD/Lip_tran_initial_ext.parm
+#-----------------------------------------------------------------------------
+cd $PBS_O_WORKDIR
+
+setenv MPIRUN "/users2/local/mpich2-1.4.1p1_intel/bin/mpirun "
+set NPROCS=`cat $PBS_NODEFILE | wc -l`
+
+setenv FGPROCS 4
+setenv POT GB
+setenv PREFIX file
+setenv OUT1FILE YES
+
+$MPIRUN -machinefile $PBS_NODEFILE -np $NPROCS $UNRES_BIN
+
+if ( `grep -c pdbref file.inp` ) then
+ awk '{if ( NF == 14 ) print}' file_GB000.stat > md.stat
+else
+ awk '{if ( NF == 10 ) print}' file_GB000.stat > md.stat
+endif
+
+../files/matplotlib_fit_hist.py $dimen3
+rm md.stat
+
+if ( -f "file_MD000.pdb" ) then
+ mkdir tmp
+ /users2/local/pymol_1.6/pymol -c ../files/movie.pml
+ ffmpeg2theora tmp/aa%4d.png -o md.ogv
+ rm -rf tmp
+else
+ /users2/czarek/UNRES/git3_tmp/build/bin/xdrf2pdb-mult one file.seq file_MD000.cx
+ mkdir tmp
+ /users2/local/pymol_1.6/pymol -c ../files/movie.pml
+ ffmpeg2theora tmp/aa%4d.png -o md.ogv
+ rm -rf tmp file_MD000.pdb
+endif
+
+touch finished

diff --git a/files/pbs_new.csh b/files/pbs_new.csh
new file mode 100755 (executable)
index 0000000..5d733f6
--- /dev/null
+++ b/files/pbs_new.csh
@@ -0,0 +1,38 @@
+#PBS -N test_server
+#PBS -q express
+#PBS -l nodes=1:ppn=4
+
+#-----------------------------------------------------------------------------
+setenv UNRES_BIN /users2/czarek/UNRES/git3_tmp/build/bin/unresMD-mult_ifort_MPI_E0LL2Y.exe
+#-----------------------------------------------------------------------------
+setenv DD /users2/czarek/UNRES/git3_tmp/unres/PARAM
+setenv BONDPAR $DD/bond_AM1_ext_dum.parm
+setenv THETPAR $DD/theta_abinitio-ext-old.parm
+setenv THETPARPDB $DD/thetaml_ext.5parm
+setenv ROTPARPDB $DD/scgauss_ext.parm
+setenv ROTPAR $DD/rotamers_AM1_aura_ext.10022007.parm
+setenv TORPAR $DD/tor_opt_iter1_7p_old-ext.parm
+setenv TORDPAR $DD/pot_tord_G631_DIL_ext.parm
+setenv ELEPAR $DD/electr_631Gdp_ext.parm
+setenv SIDEPAR $DD/sc_GB_opt_iter1_7p_old-ext_lip.parm
+setenv FOURIER $DD/fourier_opt_iter1_7p_old-ext.parm
+setenv SCCORPAR $DD/sccor_am1_pawel_ext.dat
+setenv SCPPAR $DD/scp_ext.parm
+setenv PATTERN $DD/patterns.cart
+setenv LIPTRANPAR $DD/Lip_tran_initial_ext.parm
+#-----------------------------------------------------------------------------
+cd $PBS_O_WORKDIR
+
+setenv MPIRUN "/users2/local/mpich2-1.4.1p1_intel/bin/mpirun "
+set NPROCS=`cat $PBS_NODEFILE | wc -l`
+
+setenv FGPROCS 4
+setenv POT GB
+setenv PREFIX file
+setenv OUT1FILE YES
+
+$MPIRUN -machinefile $PBS_NODEFILE -np $NPROCS $UNRES_BIN
+
+/users2/local/pymol_1.6/pymol -c ../files/pdb.pml
+
+touch finished